Merge pull request #121 from fmalmeida/dev

Wrap up v3.3.3

.github/workflows/test_pr_docker.yml

@@ -1,39 +1,46 @@
 name: Testing new PR with docker
 on:
  pull_request:
- branches: master
- types: [ ready_for_review, synchronize, reopened ]
+ branches: [master, dev]
+ types: [ opened, synchronize, reopened ]
 
 jobs:
  run_nextflow:
  name: Run pipeline for the upcoming PR
  runs-on: ubuntu-latest
- env:
- DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
- DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
-
+
  steps:
-
- - name: Check out pipeline code
- uses: actions/checkout@v2
-
- - name: Install Nextflow
- env:
- CAPSULE_LOG: none
- run: |
- wget -qO- get.nextflow.io | bash
- sudo mv nextflow /usr/local/bin/
- 
- - name: Clean environment
- run: |
- sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
- sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
- 
- - name: Build bacannot database
- run: |
- nextflow run main.nf -profile docker --get_dbs --output bacannot_dbs --max_cpus 2 --max_memory '6.GB' --max_time '6.h'
- rm -rf bacannot_dbs/antismash_db bacannot_dbs/kofamscan_db bacannot_dbs/prokka_db/PGAP_NCBI.hmm # remove unused in quicktest to diminish size
-
- - name: Run the pipeline
- run: |
- nextflow run main.nf -profile docker,quicktest --bacannot_db bacannot_dbs
+
+ - name: Check out pipeline code
+ uses: actions/checkout@v2
+
+ - name: Install Nextflow
+ env:
+ CAPSULE_LOG: none
+ run: |
+ wget -qO- get.nextflow.io | bash
+ sudo mv nextflow /usr/local/bin/
+
+ - name: Clean environment
+ run: |
+ sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+ sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+ - name: Get database
+ run: |
+ nextflow run main.nf -profile docker --get_zenodo_db --output ./ --max_memory '6.GB' --max_cpus 2
+ nextflow run main.nf -profile docker --get_zenodo_db --output ./ --max_memory '6.GB' --max_cpus 2 -resume
+ nextflow run main.nf -profile docker --get_zenodo_db --output ./ --max_memory '6.GB' --max_cpus 2 -resume
+ sudo rm -r work .nextflow*
+ yes | docker system prune
+
+ - name: Run quicktest profile
+ run: |
+ nextflow run main.nf -profile docker,quicktest --bacannot_db $( realpath ./bac* ) --output ./results --max_memory '6.GB' --max_cpus 2
+ sudo rm -r work .nextflow*
+ yes | docker system prune
+
+ - name: View results
+ run: |
+ sudo apt-get install -y tree
+ tree ./results

.zenodo.json

@@ -2,7 +2,7 @@
  "description": "<p>The pipeline</p>\n\n<p>bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, secondary metabolites, genomic islands, prophages, ICEs, KO, and more, while providing nice an beautiful interactive documents for results exploration.</p>", 
  "license": "other-open", 
  "title": "fmalmeida/bacannot: A generic but comprehensive bacterial annotation pipeline", 
- "version": "v3.3.2", 
+ "version": "v3.3.3", 
  "upload_type": "software",
  "creators": [
  {